All players can start to build or train a vehicle or infantry from anywhere from a sidebar, however once complete it instantly goes on hold.

In the case of a vehicle, clicking the held vehicle will make it come out from the WF, in the case of infantry the player's current character dies and he gets respawned as the new one, a death is counted.

alternatively a player can return to a barracks and switch to their newly prepared character without a death penalty.

What this will allow is to bring in build times in a fair and balanced way as you can prepare a unit from any point you are on a map, it also allows you to build a proportion of the unit if you don't have the full cash, only one vehicle and one infantry should be allowed at a time however.

Nice suggestion, but we already have a system that may work out better and is more faithful to RTS build system. You don't walk up portals and become instantly that unit or anything; Commander chooses what unit you will become. It takes some time before you're fully trained and that depends on the unit cost. As long as you are alive you cannot become another unit.

It wouldn't be fun if a stupid Commander could kill a player in middle of combat.

Yes, but that could be solved like this: A commander selects you and begins to train you as a chemical warrior.

Then a window will appear at your screen were it says: Commander "Insert Name here" is suggesting a character change to chemical warrior, Accept - don't accept. If you accept, you will be transformed into a chemical warrior when it's ready, if you don't accept, the training sequence will be aborted.
And about a commander spamming another player with training suggests could be solved by make a time limit before he can suggest a player to change unit or that if the commander suggests too many times in a short time, he will be baned.

Ahh, you mean like my idea but reverted so that instead that the commander request the answer from the player, the player requestes answer from the commander. Well, when I think about it that would work even better.
Smart idea!

As for other commander features, how about implementing the command interface RTS style, click on the player unit you want to order, and then click the position to go to or target to attack, for the player a beacon will indicate the last order.

multiple orders can be done simply by holding Alt and then clicking the orders in succession, beacons of a different colour will indicate the orders with a line inbetween them indicating their order, a normal coloured beacon will indicate the first or next order to carry out.

If you want to change the order, you simply give another command without the Alt button.